Volume 10 Supplement 3
Edited by Shoba Ranganathan, Frank Eisenhaber, Joo Chuan Tong and Tin Wee Tan
Asia Pacific Bioinformatics Network (APBioNet) Eighth International Conference on Bioinformatics (InCoB2009). Go to conference site.
Singapore7-11 September 2009
The 2009 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation dating back to 1998, was organized as the 8th International Conference on Bioinformatics...
Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymor...
Oligonucleotide design is known as a time-consuming work in bioinformatics. In order to accelerate and be efficient the oligonucleotide design process, one of widely used approach is the prescreening unreliabl...
Polymerase chain reaction (PCR) is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools...
Activation of PPARs has been reported to inhibit the proliferation of malignant cells from different lineages. They are involved in transcription regulation of genes upon activation by a ligand. The binding of...
Caspases belong to a class of cysteine proteases which function as critical effectors in cellular processes such as apoptosis and inflammation by cleaving substrates immediately after unique tetrapeptide sites...
Insertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB)...
DNA barcoding provides a rapid, accurate, and standardized method for species-level identification using short DNA sequences. Such a standardized identification method is useful for mapping all the species on ...
DNA triplexes can naturally occur, co-localize and interact with many other regulatory DNA elements (e.g. G-quadruplex (G4) DNA motifs), specific DNA-binding proteins (e.g. transcription factors (TFs)), and mi...
The characterisation, or binning, of metagenome fragments is an important first step to further downstream analysis of microbial consortia. Here, we propose a one-dimensional signature, OFDEG, derived from the...
Alternative splicing (AS) is a primary mechanism of functional regulation in the human genome, with 60% to 80% of human genes being alternatively spliced. As part of the bovine genome annotation team, we have ...
Mitochondrial sequence variation provides critical information for studying human evolution and variation. Mitochondrial DNA provides information on the origin of humans, and plays a substantial role in forens...
Next-generation sequencing technologies provide exciting avenues for studies of transcriptomics and population genomics. There is an increasing need to conduct spliced and unspliced alignments of short transcr...
Grouping genes into clusters on the basis of similarity between their expression profiles has been the main approach to predict functional modules, from which important inference or further investigation decis...
Gene expression similarity measuring methods were developed and applied to search rapidly growing public microarray databases. However, current expression similarity measuring methods need to be improved to ac...
It has been a long-standing biological challenge to understand the molecular regulatory mechanisms behind mammalian ageing. Harnessing the availability of many ageing microarray datasets, a number of studies h...
The reconstruction of gene regulatory networks from high-throughput "omics" data has become a major goal in the modelling of living systems. Numerous approaches have been proposed, most of which attempt only "...
Pseudomonas putida KT2440 (P. putida KT2440) is a highly versatile saprophytic soil bacterium. It is a certified bio-safety host for transferring foreign genes. Therefore, the bacterium is used as a model organis...
The PolyGalacturonase-Inhibiting Proteins (PGIP) of plant cell wall limit the invasion of phytopathogenic organisms by interacting with the enzyme PolyGalacturonase (PG) they secrete to degrade pectin present ...
Mitochondria play a vital role in the energy production and apoptotic process of eukaryotic cells. Proteins in the mitochondria are encoded by nuclear and mitochondrial genes. Owing to a large increase in the ...
In this paper, we introduce a novel inter-range interaction integrated approach for protein domain boundary prediction. It involves (1) the design of modular kernel algorithm, which is able to effectively expl...
Proteins are dynamic macromolecules which may undergo conformational transitions upon changes in environment. As it has been observed in laboratories that protein flexibility is correlated to essential biologi...
Protein-DNA interactions are essential for fundamental biological activities including DNA transcription, replication, packaging, repair and rearrangement. Proteins interacting with DNA can be classified into ...
It is known that the highly pathogenic avian influenza A virus H5N1 binds strongly and with high specificity to the avian-type receptor by its hemagglutinin surface protein. This specificity is normally a barr...
Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics t...
The steady-state behaviour of gene regulatory networks (GRNs) can provide crucial evidence for detecting disease-causing genes. However, monitoring the dynamics of GRNs is particularly difficult because biolog...
Eukaryotic genomes are packaged into chromatin, a compact structure containing fundamental repeating units, the nucleosomes. The mobility of nucleosomes plays important roles in many DNA-related processes by r...
Time delays are often found in gene regulation though most techniques of building gene regulatory networks are not capable of capturing such phenomena. Here we look at the delays in the DNA repair system of Mycob...
Gene regulation is a key mechanism in higher eukaryotic cellular processes. One of the major challenges in gene regulation studies is to identify regulators affecting the expression of their target genes in sp...
Human immunodeficiency virus-1 (HIV-1) has a minimal genome of only 9 genes, which encode 15 proteins. HIV-1 thus depends on the human host for virtually every aspect of its life cycle. The universal language ...
Rate-limiting enzymes, because of their relatively low velocity, are believed to influence metabolic flux in pathways. To investigate their regulatory role in metabolic networks, we look at the global organiza...
Parkinson's disease (PD) is one of the most common neurodegenerative disorders, clinically characterized by impaired motor function. Since the etiology of PD is diverse and complex, many researchers have creat...
Lysosomal α-mannosidase is an enzyme that acts to degrade N-linked oligosaccharides and hence plays an important role in mannose metabolism in humans and other mammalian species, especially livestock. Mutation...
Medical and biological data are commonly with small sample size, missing values, and most importantly, imbalanced class distribution. In this study we propose a particle swarm based hybrid system for remedying...
A disease-causing mutation refers to a heritable genetic change that is associated with a specific phenotype (disease). The detection of a mutation from a patient's sample is critical for the diagnosis, treatm...
The development of high throughput experimental technologies have given rise to the "-omics" era where terabyte-scale datasets for systems-level measurements of various cellular and molecular phenomena pose co...
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